The goal of the Immunohistochemistry and Molecular Pathology Core is to facilitate immunohistochemical and molecular genetic analyses of tumor materials by:

• Performing routine immunohistochemical (IHC) analyses of tumor sections.
• Performing IHC analysis of tissue arrays produced by the Cancer Center's Tissue Core.
• Develop new IHC and in situ hybridization (FISH) based assays in collaboration with Cancer Center members.
• Develop and share protocols for IHC and molecular analysis of section-based tumor materials.
• Perform section-based FISH analyses for genomic copy number.
• Collaborate with members in microdissection and extraction of DNA and RNA from tumor sections.
• Perform genomic mapping onto metaphase chromosomes of human and mouse DNA clones.
• Perform human and mouse comparative genomic hybridization.

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Services

Immunohistochemistry

Routine Immunohistochemistry Staining

Standard protocols have been developed for a number of antibodies (see list >). Sections of paraffin-embedded tissue to be stained should be brought to the Core laboratory, 2340 Sutter Street, Room S-441, between 8:00 am and 4:30 pm Monday-Friday. The tissue must be accompanied by a completed work order form. If tissue sections are not available, the paraffin block may be brought to the Core laboratory for sectioning.

Protocol Development for Novel Antibodies

The laboratory assists in the development of protocols for novel antibodies. Investigators should meet with Core Director Rick Baehner (415.885.7586) to discuss this service. The investigator should be prepared to provide the antibody, references of its use in immunohistochemistry, positive and negative controls, information from Western analyses, and sections of the tissues to be stained.

Molecular Pathology

FISH for Copy Number
FISH analysis of research and clinical specimens for copy number of specific loci, and specific translocations, on a cell-by-cell basis. This is available for cultured cells (interphase or metaphase), and for paraffin sections of formalin-fixed tissue.

FISH Mapping of DNA Probes
FISH mapping of unique sequence DNA probes to metaphase chromosomes. Metaphase spreads of human and mouse chromosomes are available through the laboratory, while other species must be prepared prior to mapping. Contact the Core for details on metaphase preparations. DNA probes should be at a concentration of 400-800 ug/ul in TE or water. 510 ugs of DNA is required.

Comparative Genomic Hybridization
CGH analysis of human and murine specimens. CGH from DNA extracted from fresh/frozen material is of higher quality than from paraffin sections. DOP-PCR amplification of DNA extracted from fresh/frozen or paraffin sections is also available (see Appendices). Protocol instructions for DNA extraction from paraffin can be found on the Waldman Lab website.

Preparation of Metaphase Spreads for Cytogenetic Analysis
The laboratory can culture and prepare metaphase spreads if cultured cells are provided. Although the laboratory will accept slides, preferably the lab will prepare the metaphase spreads and the user need only supply the growing cell line. Cell cultures should be delivered to the lab within 24 hours after passage. Bring cell cultures to the lab no later than 12 noon Monday-Friday. Cells can be brought to the Mt. Zion Clinical Lab to Sandy DeVries, 2340 Sutter Street, Room S441. Phone: 476-3822.

Laser Capture Microdissection
An Arcturus Laser Capture Microdissection instrument is available for use by Cancer Center members, with on-site training provided. Sign-up for the LCM can be accessed from the Laboratory of Cell Analysis. First-time users should contact LCA staff to arrange instrument time. Established users may view availability and schedule time on most LCA instruments through Meeting Maker by using the login name "lcaguest" and the password "lcaguest". Please include your name and contact information when scheduling. If you require assistance from an operator, call Sandy DeVries at 476-3822 to have the appointment booked for you.

Education

Training in IHC techniques is informal and hands-on, and takes place as time permits. Contact Loretta Chan to schedule a session. Core personnel are also available to train researchers in molecular cytogenetic techniques, comprising both didactic sessions and hands-on laboratory experience. By arrangement, trained personnel from Cancer Center labs may use Core equipment and lab space for their own molecular cytogenetic analyses.

Additional Resources
A searchable database of core facilities at all UCSF campus locations, provided by the Clinical and Translational Science Institute at UCSF, is available here.